To answer your question in short, you can't change notification preferences for all/some users in Yammer. What you could do is create an Exchange Transport Rule to block incoming emails from Yammer with the same subject as the notification email.
If this was indeed a highlights email, which goes out weekly, then ideally the email would notify the users of not only just one discussion, but multiple posts from communities that the users aren't member of. If the email notification is only about one post, then I doubt it's a highlight email. One way to test that theory is validate the persistence of the issue. For e.g. does creating another discussion in the same community send out emails to all users again? Is the email sent immediately or before the end of the week? If you disable the highlights notification settings for a single user, can you reproduce the issue again? Was the notification email addressed to individual user or a distribution list? Did the discussion tag any distribution list in it?
@David Barcelona
